Deliverables
Upon assembly of a functional DNA pore, which is verified to insert itself in biological membrane environments, the pore will be analysed using electron cryo-tomography. Subsequently, 4D-models will be created.
4D-model of archaellumUpon expression, purification and biochemical analysis of several wildtype and mutated archaellum subunits, the proteins will be analysed using electron cryo-microscopy. We will use the archaellum proteins from different archaea such as S. acidocaldarius, P.furiosus, M. jannaschii and Archaeoglobus fulgidus. We will also image the intact archaellar motor in situ in Haloferax volcanii cells. It is expected this variety of model organisms will ensure that structural information can be obtained. Subsequently, 4D-models will be created: a description of the mechanism that accounts for function.
Based on existing DNA origami design software a novel bioinformatic toolkit will be created to enable the automated protein embedding function into the DNA scaffold using the 4D models from WP3
A website that will facilitate internal and external communication and dissemination.
A Data Management Plan will be elaborated within the first six months of the project, guaranteeing an appropriate disclosure of research data to the public and standardised data management within the project. The types of data that will be generated and collected within the project comprise design data (oligonucleotide sequences, technical drawings, etc.), laboratory test data (images, reaction parameters, etc.), software and metadata (final results/scientific insights, documentation, reports, publications, etc.). Three different levels of confidentiality will be defined according to IP issues and marketing strategies: classified data, IPR relevant data and public data.
Publications
Author(s):
Lena Hoffmann, Katrin Anders, Lisa F. Bischof, Xing Ye, Julia Reimann, Sunia Khadouma, Trong K. Pham, Chris van der Does, Phillip C. Wright, Lars-Oliver Essen, Sonja-Verena Albers
Published in:
Journal of Biological Chemistry, Issue 294/18, 2019, Page(s) 7460-7471, ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology Inc.
DOI:
10.1074/jbc.ra119.007709
Author(s):
Tadija Kekic, Ivan Barisic
Published in:
Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 1191-1201, ISSN 2001-0370
Publisher:
Elsevier
DOI:
10.1016/j.csbj.2020.05.016
Author(s):
Yasaman Ahmadi, Ashley L. Nord, Amanda J. Wilson, Christiane Hütter, Fabian Schroeder, Morgan Beeby, Ivan Barišić
Published in:
Small, Issue 16/22, 2020, Page(s) 2001855, ISSN 1613-6810
Publisher:
Wiley - V C H Verlag GmbbH & Co.
DOI:
10.1002/smll.202001855
Author(s):
Zhengqun Li, Yoshiaki Kinosita, Marta Rodriguez-Franco, Phillip Nußbaum, Frank Braun, Floriane Delpech, Tessa E. F. Quax, Sonja-Verena Albers
Published in:
mBio, Issue 10/3, 2019, Page(s) e00377-19, ISSN 2150-7511
Publisher:
American Society for Microbiology
DOI:
10.1128/mBio.00377-19
Author(s):
Morgan Beeby, Josie L Ferreira, Patrick Tripp, Sonja-Verena Albers, David R Mitchell
Published in:
FEMS Microbiology Reviews, Issue 44/3, 2020, Page(s) 253-304, ISSN 0168-6445
Publisher:
Blackwell
DOI:
10.1093/femsre/fuaa006
Author(s):
Yasaman Ahmadi, Ivan Barisic
Published in:
Journal of Visualized Experiments, Issue 143, 2019, ISSN 1940-087X
Publisher:
MYJoVE Corporation
DOI:
10.3791/58771
Author(s):
Lena Hoffmann, Andreas Schummer, Julia Reimann, Maria F. Haurat, Amanda J. Wilson, Morgan Beeby, Bettina Warscheid, Sonja-V. Albers
Published in:
MicrobiologyOpen, Issue 6/1, 2017, Page(s) e00414, ISSN 2045-8827
Publisher:
John Wiley and Sons Inc.
DOI:
10.1002/mbo3.414
Author(s):
Yasaman Ahmadi, Elisa De Llano, Ivan Barišić
Published in:
Nanoscale, Issue 10/16, 2018, Page(s) 7494-7504, ISSN 2040-3364
Publisher:
Royal Society of Chemistry
DOI:
10.1039/C7NR09461B
Author(s):
M. Florencia Haurat, Ana Sofia Figueiredo, Lena Hoffmann, Lingling Li, Katharina Herr, Amanda J. Wilson, Morgan Beeby, Jörg Schaber, Sonja-Verena Albers
Published in:
Molecular Microbiology, Issue 103/1, 2017, Page(s) 181-194, ISSN 0950-382X
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/mmi.13550
Author(s):
Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, M. Eduard Groller, Ivan Barisic, Ivan Viola
Published in:
IEEE Transactions on Visualization and Computer Graphics, Issue 24/1, 2018, Page(s) 1014-1024, ISSN 1077-2626
Publisher:
Institute of Electrical and Electronics Engineers
DOI:
10.1109/TVCG.2017.2743981
Author(s):
H. Miao, E. De Llano, T. Isenberg, M. E. Gröller, I. Barišić, I. Viola
Published in:
Computer Graphics Forum, Issue 37/3, 2018, Page(s) 403-413, ISSN 0167-7055
Publisher:
Blackwell Publishing Inc.
DOI:
10.1111/cgf.13429
Author(s):
Elisa de Llano, Haichao Miao, Yasaman Ahmadi, Amanda J Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic
Published in:
Nucleic Acids Research, Issue 48/15, 2020, Page(s) 8269-8275, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkaa593
Author(s):
Chi-Lin Tsai, Patrick Tripp, Shamphavi Sivabalasarma, Changyi Zhang, Marta Rodriguez-Franco, Rebecca L. Wipfler, Paushali Chaudhury, Ankan Banerjee, Morgan Beeby, Rachel J. Whitaker, John A. Tainer, Sonja-Verena Albers
Published in:
Nature Microbiology, Issue 5/1, 2020, Page(s) 216-225, ISSN 2058-5276
Publisher:
Nature
DOI:
10.1038/s41564-019-0622-3
Author(s):
Dominik Esser, Lena Hoffmann, Trong Khoa Pham, Christopher Bräsen, Wen Qiu, Phillip C. Wright, Sonja-Verena Albers, Bettina Siebers
Published in:
FEMS Microbiology Reviews, Issue 40/5, 2016, Page(s) 625-647, ISSN 1574-6976
Publisher:
OXFORD UNIVERSITY PRESS
DOI:
10.1093/femsre/fuw020
Author(s):
Maximilian Sbardellati, Haichao Miao, Hsiang-Yun Wu, Eduard Gröller, Ivan Barisic, Ivan Viola
Published in:
VCBM 19: Eurographics Workshop on Visual Computing for Biology and Medicine, 2019, ISBN 978-3-03868-081-9
Publisher:
The Eurographics Association
DOI:
10.2312/vcbm.20191237
Intellectual Property Rights
Application/Publication number:
EP
16801263
Date:
2016-11-25
Applicant(s):
AIT AUSTRIAN INSTITUTE OF TECHNOLOGY GMBH
Application/Publication number:
EP
16806004
Date:
2016-11-25
Applicant(s):
AIT AUSTRIAN INSTITUTE OF TECHNOLOGY GMBH
Application/Publication number:
EP
16801262
Date:
2016-11-25
Applicant(s):
AIT AUSTRIAN INSTITUTE OF TECHNOLOGY GMBH
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